President Barack Obama presents the Presidential Medal of Freedom to retiring Defense Secretary Robert Gates on Thursday.

WASHINGTON — The Justice Department inquiry into CIA interrogations of terrorist detainees has led to a full criminal investigation into the deaths of two people while they were in custody in Iraq and Afghanistan, Attorney General Eric Holder said Thursday.

The attorney general said that he accepted the recommendation of a federal prosecutor, John Durham, who since August 2009 has conducted an inquiry into CIA interrogation practices during the Bush administration. Holder said Durham looked at the treatment of 101 detainees in U.S. custody since the Sept. 11, 2001, terrorist attacks and concluded that only these two deaths warranted criminal investigation. Holder said Durham found some of the 101 had never been held by the CIA.

Holder did not identify the two death cases. But former and current U.S. officials who requested anonymity to discuss an ongoing investigation said Durham was looking at the deaths of Gul Rahman and Manadel al-Jamadi, the Associated Press reported.

Rahman died in the early hours of Nov. 20, 2002, after being shackled to a cold concrete wall in a secret CIA prison in northern Kabul, Afghanistan, known as the Salt Pit. He was suspected of links to the terrorist group al-Qaida. Rahman is the only detainee known to have died in a CIA-run prison.

Jamadi died in 2003 at the Abu Ghraib prison in Iraq. The death has been known to the public for years, and a military autopsy declared Jamadi's death a homicide.

In June, a former Abu Ghraib prison guard at the time of Jamadi's death, Lynndie England, was ordered to testify in a grand jury investigation in Alexandria, Va. A subpoena signed by Durham for England's appearance says her testimony is needed in an investigation of federal criminal laws involving war crimes, torture and other offenses.

England, an Army reservist serving as a military police officer at Abu Ghraib, was among 11 soldiers found guilty of wrongdoing in the mistreatment of prisoners at Abu Ghraib prison in 2003 and 2004. Photographs showed England holding a restraint around a man's neck and giving a thumbs-up and pointing at the genitals of naked, hooded men, a cigarette dangling from her mouth.

England's attorney, Roy Hardy, said that England testified along with former MPs Chip Frederick and Sabrina Harman before the grand jury in June.

Another person who testified told the Associated Press that prosecutors asked about a hood placed over Jamadi's head that later disappeared, and who shackled Jamadi's arms behind his back and bound them to a barred window. This witness requested anonymity to avoid being connected publicly with the case.

On his last day as CIA director, Leon Panetta emphasized the wide scope of Durham's preliminary review.

"After extensive examination of more than 100 instances in which CIA had contact or was alleged to have had contact with terrorist detainees," the prosecutor "has determined that no further law enforcement action is appropriate in all but two discrete cases," Panetta, who will be sworn today as the new defense secretary, said in a statement. "I welcome the news that the broader inquiries are behind us. We are now finally about to close this chapter of our agency's history."

Gates bestowed highest honor

President Obama surprised Defense Secretary Robert Gates on Thursday with the Presidential Medal of Freedom, paying tribute to his four decades of public service at a regal farewell ceremony outside the Pentagon. The honor came on Gates' last day as defense secretary after more than four years in the job. The citation for the medal, the highest civilian honor the commander in chief can bestow, said that Gates has "selflessly dedicated his life to ensuring the security of the American people."

The secretary appeared humbled and genuinely surprised by the honor. "We should have known a couple of months ago that you were getting good at this covert ops stuff," he told the president with a smirk.

Gates, who served under eight presidents and as defense secretary under two, is retiring to Washington state. When Gates took the defense job in December 2006, he carried a clock with him that counted down his days in D.C.